Using Shortest longest path without analyse skeleton plugin

Usage & Issues
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#1

Hello,
I am currently writing a macro script to find the length of plant roots. In order to do so I am using the analyse skeleton plugin which allows me to find the longest shortest path. However, due to some noise in the background there are a lot of extra unwanted ROIs.
I have seen that you could also apply analyse partices on the skeleton image which outputs ROI based on size (pixel^2), but it does not give me the shortest longest path.

In my head, there are 3 different scenarios to solve this which I have not found the answer to:

  1. Is there a way to use the ROI manager data from the analyse particles and feed it into the analyse skeleton (2D/3D) plugin to find the shortest longest path of the selected ROIs?
    or
  2. Is there just a simple plugin/ built in tool in Fiji that allows me to find the shortest longest path of the ROIs?
    or
  3. Is there a way to just atomically filter in the analyse skeleton based on size (pixel^2) as in analyse particles?

Any help or suggestion is appreciated.
Thank you!

Overlay_of_analyse_particles_ROI
Overlay_of_analyse_particles_ROI1280×656 916 KB
Skeleton
Skeleton2526×1293 303 KB

#2

The analyze particles should be able to output a Masked image - that is what you run Skeletonize/analyze skeleton 2D/3D on.

#3

Hello,
the masked image worked great so thank you for this tip.
Now, I wanted to use this masked image to find the longest shortest path image using “Analyse Skeleton (2D/3D)” and overlay the shortest longest path onto my original image (like the one I previously posted).
However, everything I try doesn’t work, as my ROI manager seems to be empty.
Does “Analyse Skeleton (2D/3D)” not add the shortest longest path to the ROI manager? Or if it does, how can I do this, so I can overlay the shortest longest path to my original image?
Any help/ suggestions are appreciated.

#4

Kind of reaching back in my memory here, but there should be an option to output an image/mask of the paths. The longest-shortest one should be colored differently, or at least that was how it worked in the 3D stacks I was working with. You may need to do image math with that, or create a thresholder for THAT image (the path masks) that picks out only the longest-shortest path, then analyze particles the thresholded mask image…

Maybe.

#5

Yes, when I run analyse skeleton on my skeleton image, it produces an shortest longest path image corresponding to the result table data.
However, these are not viewable in the ROI manager after checking. The problem is if I run analyse particles on the path image the results table (from analyse skeleton) and the resulting ROI numbers (from analyse particles) do not match. So overlapping ROIs to the original images would not help me when checking if the measurements are reasonable.
I think this may be as the analyse particles and analyse skeleton find objects in a different sequence.